GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Sinorhizobium meliloti 1021

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate SMc00086 SMc00086 diheme cytochrome C-type signal peptide protein

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__Smeli:SMc00086
          Length = 304

 Score =  152 bits (384), Expect = 1e-41
 Identities = 92/265 (34%), Positives = 136/265 (51%), Gaps = 14/265 (5%)

Query: 31  GEYLARAGDCVACHSVKGGQP-----FAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDD 85
           GE +  AG CV+CHS  G +        GG  + +P GT Y  NI+PD+T GIG+++  +
Sbjct: 48  GEQIFWAGGCVSCHSAPGAKDDQRLVLTGGRTLKSPFGTFYPPNISPDETVGIGNWTLAE 107

Query: 86  FQKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPL 145
           F  A+  GV K+G+ LYP+ PY SY  ++ +D+  L+  FM  +   + A    D+ +P 
Sbjct: 108 FGDAMTRGVGKDGEHLYPSFPYGSYIRMTAKDVNDLWG-FMQTLPKSSNATPPHDLAFPY 166

Query: 146 SMRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALS 205
           ++R  L  W+ ++  D    Q     D  LARG+YLVEG GHCG CHTPR       AL 
Sbjct: 167 NVRLALGAWKLLYLSDEPRTQ-VNTADTKLARGQYLVEGPGHCGECHTPRD------ALG 219

Query: 206 NDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDHTAAFGGMTDV 265
                 +L+G+  P       ++   ++  +G WS  D+  +L  G        GG    
Sbjct: 220 GFEEDRWLAGAPNPEGEGRIPDITPSSK-SIGDWSASDIASYLETGFTPDFDTVGGSMVE 278

Query: 266 VEHSLQHLSDDDITAIARYLKSLGA 290
           V+ ++  L   D  AIA YLK+L A
Sbjct: 279 VQKNMAELPASDRDAIAAYLKALPA 303



 Score = 28.5 bits (62), Expect = 3e-04
 Identities = 26/119 (21%), Positives = 44/119 (36%), Gaps = 23/119 (19%)

Query: 124 YFMHGVAPVAQANKDSDIPWPLSM--RWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYL 181
           Y + G+  +  A   + + W L+   RW  A W G+  PD             LA G  +
Sbjct: 7   YLLSGLVLLVVAG--ASLAWWLTKPDRWDAAHWEGLGGPD-------------LANGEQI 51

Query: 182 VEGLGHCGACHTPRSITMQEKALSNDGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWS 240
               G C +CH+       ++ +   G         +P   +   N+  D   G+G W+
Sbjct: 52  F-WAGGCVSCHSAPGAKDDQRLVLTGG-----RTLKSPFGTFYPPNISPDETVGIGNWT 104


Lambda     K      H
   0.317    0.133    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 488
Number of extensions: 37
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 441
Length of database: 304
Length adjustment: 30
Effective length of query: 411
Effective length of database: 274
Effective search space:   112614
Effective search space used:   112614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory